In addition to resolving paraphyletic groups, this method also reassigns taxonomic ranks algorithmically, updating names in both cases.
[5] The GTDB system, via GTDB-Tk, has been used to catalogue not-yet-named bacteria in the human gut microbiome and other metagenomic sources.
The taxonomy is based on trees inferred with FastTree from an aligned concatenated set of 120 single copy marker proteins for Bacteria under a WAG model, and with IQ-TREE from a concatenated set of 53 (since RS207; 122 before) marker proteins for Archaea under the PMSF model.
[9] The relative evolutionary divergence (RED) metric, which determines the taxonomic ranks used, is derived from the two main trees by the PhyloRank program.
[1] Each release contains:[10] The web interface displays a tree based on the taxonomy (not the entire Newick file), down to the genome assembly level.
Both its species tree and elements of its methodology are used by taxonomists to improve the current, accepted taxonomy under the Prokaryotic Code.